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This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached to version 1 of this model (the published SBML is correct). The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including:
- the Evening Complex genes (ELF4, ELF3, LUX),
- light-regulated degradation of ELF3 by COP1,
- TOC1 as a repressor rather than an activator of LHY/CCA1.
Related Publications
Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar (2012). The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.. Mol. Syst. Biol. 8: 574.. Retrieved from: http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html
Originally submitted to PLaSMo on 2012-03-07 12:15:12
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Related items
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburgh

Roles: Project Coordinator, Vice Coordinator
Expertise: circadian rhythms, arabidopsis thaliana, Mathematical modelling, Data Management, Molecular Biology, Genetics, Deterministic modelling of gene regulation networks, Systems Biology
Tools: Transcriptomics, Proteomics, Deterministic models, Stochastic models, SBML
Projects: PlaSMo model repository
Institutions: University of Edinburgh
What is PlaSMo?
PlaSMo stands for Plant Systems-biology Modelling
Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.
Our aims
To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost
To represent these models in a declarative XML-based format, which is closer to the systems biology standard SBML
To evaluate the behaviour
...
Programme: SynthSys
Public web page: Not specified
Organisms: Arabidopsis thaliana, Ostreococcus tauri
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri
Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Studies: Arabidopsis clock model P2011, graphical diagram - PLM_1045, Arabidopsis clock model P2011.3.1 - PLM_1041, Arabidopsis clock model P2011.4.1 - PLM_1042, Arabidopsis clock model P2011.5.1 - PLM_1043, Arabidopsis clock model P2011.6.1 - PLM_1044, Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, Arabidopsis_clock_P2011 - PLM_64, Arabidopsis_clock_P2012 - PLM_70, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, AuxSim - PLM_27, AuxSim full - PLM_30, DomijanTS_AtClock2011 - PLM_50, Locke2005_CircadianClock_tanh - PLM_8, Locke2006_CircadianClock_tanh - PLM_10, OK MEP pathway 2013 - PLM_72, P2012_AJMv2_NoABA - PLM_69, Salazar2009_FloweringPhotoperiod - PLM_9, Sorokina2011_Ostreo_starch - PLM_44, Wilczek photothermal Science - PLM_48
Assays: Arabidopsis clock model P2011, graphical diagram - PLM_1045, version 1, Arabidopsis clock model P2011.1.2 - PLM_71, version 1, Arabidopsis clock model P2011.2.1 - PLM_71, version 2, Arabidopsis clock model P2011.3.1 - PLM_1041, version 1, Arabidopsis clock model P2011.4.1 - PLM_1042, version 1, Arabidopsis clock model P2011.5.1 - PLM_1043, version 1, Arabidopsis clock model P2011.6.1 - PLM_1044, version 1, Arabidopsis_clock_P2011 - PLM_64, version 1, Arabidopsis_clock_P2011 - PLM_64, version 2, Arabidopsis_clock_P2011 - PLM_64, version 3, Arabidopsis_clock_P2011 - PLM_64, version 4, Arabidopsis_clock_P2012 - PLM_70, version 1, Arabidopsis_clock_P2012 - PLM_70, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 1, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 3, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 4, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 5, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 6, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, version 1, AuxSim - PLM_27, version 1, AuxSim full - PLM_30, version 1, DomijanTS_AtClock2011 - PLM_50, version 1, DomijanTS_AtClock2011 - PLM_50, version 2, Locke2005_CircadianClock_tanh - PLM_8, version 1, Locke2006_CircadianClock_tanh - PLM_10, version 1, OK MEP pathway 2013 - PLM_72, version 1, P2012_AJMv2_NoABA - PLM_69, version 1, P2012_AJMv2_NoABA - PLM_69, version 2, Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2, Sorokina2011_Ostreo_starch - PLM_44, version 1, Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached
...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis_clock_P2011 - PLM_64
Organisms: Arabidopsis thaliana
Models: Arabidopsis_clock_P2011 - PLM_64, version 3, SI..., Arabidopsis_clock_P2011 - PLM_64, version 3, SU...
SOPs: No SOPs
Data files: Copasi file corresponding to PLM_64 version 3, ..., Fig. 1, outline of P2011 model, with P2010 inse..., Fig. 8, cartoon illustrating repressilator stru..., Matlab version of P2011 clock model, PLM_64_ 3, ODE file for Matlab version of P2011 clock mode...
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached
...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis_clock_P2011 - PLM_64
Organisms: No organisms
Models: Arabidopsis_clock_P2011 - PLM_64, version 4, SI..., Arabidopsis_clock_P2011 - PLM_64, version 4, SU...
SOPs: No SOPs
Data files: Fig. 1, outline of P2011 model, with P2010 inse..., Fig. 8, cartoon illustrating repressilator stru..., Matlab version of P2011 clock model, PLM_64_ 4, ODE file for Matlab version of P2011 clock mode...
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached
...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis_clock_P2011 - PLM_64
Organisms: No organisms
Models: Arabidopsis_clock_P2011 - PLM_64, version 2, SI..., Arabidopsis_clock_P2011 - PLM_64, version 2, SU...
SOPs: No SOPs
Data files: No Data files
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached
...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Snapshots: No snapshots
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: Arabidopsis_clock_P2011 - PLM_64
Organisms: No organisms
Models: Arabidopsis_clock_P2011 - PLM_64, version 1, SI..., Arabidopsis_clock_P2011 - PLM_64, version 1, SU...
SOPs: No SOPs
Data files: Describes minor errors in published Supplementa..., Fig. 1, outline of P2011 model, with P2010 inse..., Fig. 8, cartoon illustrating repressilator stru..., Matlab version of P2011 clock model, PLM_64_ 1, ODE file for Matlab version of P2011 clock mode...
Data file for PLaSMo accesssion ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Simplified model file for PLaSMo accession ID PLM_64, version 4 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 4
Originally submitted model file for PLaSMo accession ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 4
Simplified model file for PLaSMo accession ID PLM_64, version 3 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 3
Originally submitted model file for PLaSMo accession ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 3
Simplified model file for PLaSMo accession ID PLM_64, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 2
Originally submitted model file for PLaSMo accession ID PLM_64, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 2
Simplified model file for PLaSMo accession ID PLM_64, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 1
Originally submitted model file for PLaSMo accession ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Millar, Andrew (ex-PlaSMo models)
Studies: Arabidopsis_clock_P2011 - PLM_64
Modelling analyses: Arabidopsis_clock_P2011 - PLM_64, version 1
Abstract (Expand)
Authors: A. Pokhilko, A. P. Fernandez, K. D. Edwards, M. M. Southern, K. J. Halliday, A. J. Millar
Date Published: 6th Mar 2012
Publication Type: Not specified
PubMed ID: 22395476
Citation: Mol Syst Biol. 2012 Mar 6;8:574. doi: 10.1038/msb.2012.6.